<b><i>Background/Aims:</i></b> The <i>HESX1</i> gene is essential in forebrain development and pituitary organogenesis, and its mutations are the most commonly identified genetic cause of septo-optic dysplasia (SOD). The <i>PROP1 </i>gene is involved in anterior pituitary cell lineage specification and is commonly implicated in non-syndromic combined pituitary hormone deficiency (CPHD). We aimed to assess the involvement of <i>HESX1</i> and <i>PROP1</i> mutations in a cohort of patients with SOD and CPHD. <b><i>Methods:</i></b> Six patients with sporadic SOD and 16 patients with CPHD from 14 pedigrees were screened for mutations in <i>HESX1</i> and <i>PROP1 </i>genes by exon sequencing. Half of the CPHD patients had variable associated clinical characteristics, such as hearing loss, orofacial cleft, kidney disorder or developmental delay. Novel variants were evaluated in silico and verified in SNP databases. <b><i>Results:</i></b> A novel heterozygous p.Glu102Gly mutation in the <i>HESX1</i> gene and a novel homozygous p.Arg121Thr mutation in the <i>PROP1</i> gene were detected in 2 pedigrees with CPHD. A small previously reported deletion in <i>PROP1</i> c.301_302delAG was detected in a separate patient with CPHD, in heterozygous state. No mutations were identified in patients with SOD. <b><i>Conclusions:</i></b> Our results expand the spectrum of mutations implicated in CPHD. The frequency of 15% of the <i>PROP1</i> mutations in CPHD was low, likely due to the clinical heterogeneity of the cohort.